Over the past several decades, humankind has been confronted with a plethora of infectious pathogens that present differential diagnostic challenges due to similar on-set clinical symptoms and lead to diseases that afflict millions of people globally. Clinicians and field health care workers have long desired portable diagnostic tools that rapidly provide multiple differential diagnostic data in order to implement targeted therapeutic intervention and monitor the trend of disease transmission through epidemiological surveillance. It is apparent that a need exists for a detection assay in fulfillment of this quest. Thus, several diagnostic tests including nucleic acid-based multiplex isothermal amplification methods have been developed and used to detect various pathogens. These detection formats, including some isothermal platforms, are rigid and inflexible and do not allow for rapid simultaneous detection and identification of pathogens. Also, such platforms hardly enable simultaneous quantitation of the pathogen load in an infected person. A further shortcoming of existing methods is their intermittent open-tube characteristic of performance that renders them prone to contamination. Therefore, the objective of this method is to provide a versatile and flexible pathogen detection platform that enables shuffling of detection components and real-time isothermal multiplexing for rapid detection, identification, and quantitation of bacteria, viruses, and protozoans, among other pathogens. A further object of this invention is to provide a commercially practicable detection method that is portable, inexpensive, and field-deployable. Furthermore, it is the objective of the present invention to provide a comparably sensitive and specific multiplexing detection system that will contribute to national and global public health safety; this would contribute to ensuring early diagnosis of multiple infectious diseases and simultaneous identification of their causative agents, thereby enabling timely therapeutic intervention as well as ensuring national and global public health security.